[Bioperl-l] Re: Information regarding BioPerl Transfac module

Stefan Kirov skirov at utk.edu
Fri Jul 15 14:20:42 EDT 2005

Please address all questions to the bioperl list (if appropriate) and 
not to me personally.
Bio:::Matrix::PSM::IO can parse only the matrix.dat file at the moment 
and I have no intention of extending it. As for TFBS::DB::LocalTRANSFAC- 
it is not part of BioPerl in the moment and I believe  qustions should 
be addressed to Boris Lehnard or Leonardo Ramirez.  But it is clear to 
me from the documentation, that it also parses only matrix.dat (see NAME 

Nagesh Chakka wrote:

> Dear Stefan Kirov,
> I am Nagesh doing my PhD in Medical Sciences at Australian National 
> University. I have read some of your posting in the BioPerl mailing 
> list and thought of writing to you as I was not able to get the 
> information I wanted. I wanted to know whether we can achieve a simple 
> task of getting the information (about the name of the TF, Cell 
> specificity, tissue expression and other information) from the .dat 
> file if we know the matrix ID information using the 
> TFBS::DB::LocalTRANSFAC. I havent seen any method that returns what I 
> am interested in. So are there any other modules to achieve this task. 
> I also had a look at the Bio::Matrix::PSM::IO (could not find what I 
> wanted).
> Thanks very much for your attention. Any information related to this 
> would be highly appreciated.
> Regards
> Nagesh Chakka
> PhD Student
> John Curtin School of Medical Research
> Australian National University
> PO Box 334, Canberra ACT 2601
> Phone: +61-2-6125-8303
> Fax: +61-2-6125-0415

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